Postprocessing

[DaniMagyar]

Hi. I would like to use the Postprocessing module to remove double detected spikes. I run Kilosort3 from Matlab, then try to run the module in cmd but I get this error message:

ecephys spike sorting: kilosort postprocessing module Loading data... Removing within-unit overlapping spikes... Traceback (most recent call last): File "C:\Users\dmagyar\AppData\Local\Programs\Python\Python310\lib\runpy.py", line 196, in _run_module_as_main return _run_code(code, main_globals, None, File "C:\Users\dmagyar\AppData\Local\Programs\Python\Python310\lib\runpy.py", line 86, in _run_code exec(code, run_globals) File "C:\Users\dmagyar\Documents\Matlab_toolboxes_DM\ecephys_spike_sorting\ecephys_spike_sorting\modules\kilosort_postprocessing__main__.py", line 94, in main() File "C:\Users\dmagyar\Documents\Matlab_toolboxes_DM\ecephys_spike_sorting\ecephys_spike_sorting\modules\kilosort_postprocessing__main.py", line 84, in main output = run_postprocessing(mod.args) File "C:\Users\dmagyar\Documents\Matlab_toolboxes_DM\ecephys_spike_sorting\ecephys_spike_sorting\modules\kilosort_postprocessing\main__.py", line 44, in run_postprocessing remove_double_counted_spikes(spike_times, File "C:\Users\dmagyar\Documents\Matlab_toolboxes_DM\ecephys_spike_sorting\ecephys_spike_sorting\modules\kilosort_postprocessing\postprocessing.py", line 73, in remove_double_counted_spikes for idx1, unit_id1 in enumerate(unit_list[order]): IndexError: index 175 is out of bounds for axis 0 with size 175

For me it seems like unit_list is 1 number smaller than it should be. If I change line 58 in postprocessing.py from "unit_list = np.arange(np.max(spike_clusters)+1)" to "unit_list = np.arange(np.max(spike_clusters)+2)" the module works.

I dont really understand this problem, I'm pretty new to programming.

Thank you for your help.

[jsiegle]

Have you done any manual curation of this dataset? It's possible that's creating a discrepancy between the cluster IDs and the templates files (which the order is computed from).

[DaniMagyar]

Thank you for your comment. It turned out that Kilosort3 caused the discrepancy between the cluster IDs and the template files, probably because there were no spikes on multiple channels.